Hello dduminy,
That is very strange.
We tried the same test on the same setup (S32K3X8EVB-Q289, the same MCU maskset, and the same manufacturing batch).
RadekS_0-1709296166524.png
We restart MCU and wait at the breakpoint at the beginning of the main() and drive the pin directly by Lauterbach probe. We measured voltage at PTD21 pin at J357 connector and also on GPIO pin matrix breakboard.
RadekS_1-1709296334845.png
The output voltage fits with the pin output level and the same levels was detected at the pin input.
RadekS_2-1709296472730.png
RadekS_3-1709296503067.png
Are you sure that you do not have any load/short externally connected to the PTD21?
RadekS_4-1709296868466.png
Best regards
RadekS